rs2250072

Variant names:

• chr15-48092710-A-G
• rs2250072

Your query was ambiguous. Multiple possible variants found:

• chr15-48092710-A-G
• chr15-48092710-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.339 in 152,098 control chromosomes in the GnomAD database, including 17,227 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.34 (17227 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.429

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51380 AN: 151980 Hom.: 17164 Cov.: 32

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.0833

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0803

Gnomad OTH AF: 0.290

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.339 AC: 51508 AN: 152098 Hom.: 17227 Cov.: 32 AF XY: 0.338 AC XY: 25108 AN XY: 74378

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.0833

Gnomad4 EAS AF: 0.897

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.0414

Gnomad4 NFE AF: 0.0803

Gnomad4 OTH AF: 0.297

Alfa AF: 0.131 Hom.: 4741

Bravo AF: 0.389

Asia WGS AF: 0.664 AC: 2307 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.57
DANN	Benign	0.61

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2250072; hg19: chr15-48384907;